Lecture 2 Biological Organic Mo

Homework questions to be emailed to valenciabiologyhw@gmail.com

1. List the 4 major classes of biomolecules
2. Explain what distinguishes lipids from other major classes of macromolecules
3. Describe the characteristics that distinguish proteins from the other major classes of macromolecules and explain the biologically important functions of proteins
4. Define denaturation and explain how proteins my be denatured
5 Describe the characteristics that distinguish nucleic acids from the other major groups of macromolecules
Lecture 2

Biological Organic Molecules
A. Organic Molecules
Why carbon?
Functional Groups
Composed of subunits
Building Blocks
B. Major Biological Molecules
Carbohydrates
Lipids
Proteins Nucleic Acids

Why Carbon?
Carbons four electrons can participate in up to four covalent bonds
Carbon can bond to each other forming straight chain, branched chains, rings.
carbon can bond to:
hydrogen ( forms one bond)
oxygen ( two bonds)
nitrogen (three bonds )
sulfur (two bonds ) phosphorus (five bonds)

Carbon
In addition to water, carbon is the “key” to life
Uniqueness lies in it’s size and ability to accept 4 electrons
Most significantly, it is able to readily bond with other carbon atoms
C-C bond is both strong and stable
In addition carbon is routinely found in certain combinations with other atoms

The Chemical Elements of Life: A Review
The versatility of carbon
Makes possible the great diversity of organic molecules

Six functional groups are important in the chemistry of life
Hydroxyl
Carbonyl x
Carboxyl
Amino
Sulfhydryl x
Phosphate

Some important functional groups of organic compounds

-CH3 Methyl
-OH Hydroxyl
-COOH Carboxyl
-C=O Carbonyl
-PO32- Phosphate
-NH2 Amino

4 Major classes depending on monomeric components
Sugars

Fatty Acids

Amino Acids
Nucleotides
Hydrocarbons
Hydrocarbons usually occur in specific types of rocks, principally shales. Organic remains gradually rot, and are buried and compressed by new sediments. Heat and pressure may change the carbon from the rocks into hydrocarbons. Oil tends to form in rocks whose carbon comes largely from marine plants and animals. Gas tends to form in deposits which contain carbon largely from land plants

The hydrocarbons gradually seep from the source rock and travel along the path of least resistance. Since gas and oil are lighter than water, they tend to rise, collecting in pockets formed by rock traps. Traps occur where a layer of rock prevents the hydrocarbons from moving further upward.

Alkanes are produced by refining petroleum, shale oil, or coal. Many alkanes are used for fuels: methane as natural gas, propane in gas grills, and butane in lighters. Gasoline is a complex mixture of many alkanes. When alkanes react with chlorine, they produce compounds that are used as paint strippers and dry cleaning fluids. The anesthetic chloroform is a chlorinated hydrocarbon.

Alkanes follow this general formula: CnH2n+2
Alkanes are hydrocarbons with only single bonds.
The name and chemical formula for the first ten "normal" alkanes:

Methane - CH4
Ethane - C2H6 Propane - C3H8 Butane - C4H10 Pentane - C5H12 Hexane - C6H14 Heptane - C7H16 Octane - C8H18 Nonane - C9H20 Decane - C10H22
Functional Groups
Functional group is an arrangement of atoms in an organic molecule that is responsible for most of the chemical properties of that molecule.
Chemical properties of organic molecules == primarily function of specific functional groups.

Functional Groups continued
When a class of compounds is characterized by a certain functional group,
the letter R can be used to stand for the remainder of the molecule.
R-O-H (an alcohol)
.

Biological Organic Molecules Are composed of subunits
( Building Blocks).
monomers (mono = one) combined to make polymers ( poly = many).
very large organic molecules are called macromolecules ( macro = large)

Common combining reaction
A common combining reaction is an exchange reaction call dehydration synthesis (de = from; hydra = water).
(removal of a molecule water H20)
See Fig. 2.6
Reverse reaction is hydrolysis( hydra = water; lysis = break down)

Alcohols—an alkane with a hydroxyl group added hydroxyl group of alcohols is hydrophilic (water-loving) attracts water. Makes it a good organic solvent

CH3-0H
The main alcohol you need to be aware of today is

CH3CH2CH2OH—or Propanol that has 3 OH’s--Glycerol

Figure 5.12 Examples of saturated and unsaturated fats and fatty acids

Lipids
( lip = fat)
lipids are nonpolar molecules = insoluble in water
Simple Lipids
called fats or triglycerides
glycerol
3 carbons attached to three hydroxyl groups (- OH)
fatty acids
consist long hydrocarbon chains ending in carboxyl group (-COOH).

Lipids contain
Fatty acid molecule and glycerol hydroxyl
combined with ester linkage
saturated fat = no double bonds
unsaturated fat = double bonds kinks chain
Fatty Acid Molecule
Fig. 2.7

Complex lipids
phospholipids
glycerol
two fatty acids
phosphate group

Phospholipids continued
Phosphate group give lipid a polar head.
(hydrophilic water loving)
Fatty acids are hydophobic (water-fearing).
In water phospholipids form a bilayer = membrane polar group facing out, fatty acids in.

Lipids and Water
Fatty acids have a hydrophobic tail
Causes them to form a film on water or, a sealed sphere (a micelle)
+ hydrophilic head

Figure 5.14 Bilayer structure formed by self-assembly of phospholipids in an aqueous environment

Table 5.1 An Overview of Protein Functions
Figure 5.16 The catalytic cycle of an enzyme

Figure 5.17 The 20 amino acids of proteins

Figure 5.18 Making a polypeptide chain

Proteins
Proteins are essential for all aspects of cell structure and function.
Enzymes
Building block proteins = amino acids

Amino Acids
contains at least one Carboxyl group
contains at least one Amino group
Off of the alpha carbon
R = attached groups containing carbon, hydrogen, oxygen, nitrogen and some cases sulfur.
there are 20 different amino acids

Peptide Bonds
It is another dehydration synthesis
two amino acids = dipeptide
three amino acid = tripeptide
long, chain = polypeptide
folded functional polypeptide = proteinFig. 2.8

Levels of Protein Structure:
primary structure = unique sequence of amino acids linked together.
secondary structure = twisting and folding of polypeptide chain (helix and/or pleated sheets.
Figure 5.20 Exploring Levels of Protein Structure: Primary structure
Figure 5.20 Exploring Levels of Protein Structure: Secondary structure

tertiary structure = overall 3D structure
hydrogen and ionic bonds between R groups
hydrophobic interactions
disulfide bridges
quarternary structure = aggregation of two or more polypeptide chains
Fig. 2.16a

Figure 5.20 Exploring Levels of Protein Structure: Tertiary structure

Protein Tertiary and Quaternary Structure
Nucleic Acids
RNA and DNA are polynucleotides
Figure 5.20 Exploring Levels of Protein Structure: Quaternary Structure

Figure 5.22 Denaturation and renaturation of a protein

Figure 5.21 A single amino acid substitution in a protein causes sickle-cell disease

Carbohydrates
Sugars and starches
made up:
carbon
hydrogen
oxygen
C6H12O6= glucose
general formula - (CH2O)n

Carbohydrates continued
monosaccharides ( sacchar = sugar)
4 carbons = tetrose
5 carbons = pentoses
6 carbons = hexoses
glucose is a hexose important living organisms.
7 carbons = heptoses

Carbohydrates continued
disaccharides ( di = two)
two monomers formed by dehydration synthesis reaction.
sucrose = glucose and fructose
lactose = glucose and galactose
polysaccharides
10 to 100 monosaccharides joined through dehydration synthesis

Monosaccharides
(sugars)
Generic formula of -(CH2O)n
- where 3<n<8, with >2 -OH groups
Terminal aldehyde group (aldoses) or ketone group (ketoses)

monosaccharides ( sacchar = sugar)
4 carbons = tetrose
5 carbons = pentoses
6 carbons = hexoses
glucose is a hexose important in living organisms.
7 carbons = heptoses

Monosaccharide Ring Formation
In aqueous solution aldehyde or ketone group reacts with the -OH group to “close” the chain into a ring structure
Minor differences in the spatial arrangement of atoms leads to the formation of isomers.

e.g. Glucose, mannose and galactose have identical formulas (C6H12O6) but different structures
Allows for specific enzyme recognition and different biological effects

Sugar derivatives
Hydroxyl group of simple monosacharides can be replaced
Alters the physical properties of the molecule and how it reacts

Figure 5.7 Starch and cellulose structures
Figure 5.8 The arrangement of cellulose in plant cell walls

Disaccharide Formation
Hydroxyl group on the carbon that attaches to the ketone or aldehyde group
can change position
a-hydroxyl down
hydroxyl up
Also allows one monosaccharide to react with another -OH group
Forms a disaccharide
-4 Linkage

Disaccharide and Polysaccharide
Formation
The disaccharide formed depends on the type of monosaccharide involved
Glucose + Glucose = Maltose
Glucose + Galactose = Lactose
Glucose + Fructose = Sucrose

Figure 5.5 Examples of disaccharide synthesis

Polysaccharides are formed by multiple monosaccharides joining together in repeating units (e.g. Glycogen is a polysaccharide made of glucose)
Complex polysaccharides are formed by multiple different monosaccharides joining together in repeating units.
Complex polysaccharides are often linked to proteins or lipids

Figure 5.6 Storage polysaccharides of plants and animals

Structure of DNA
bases
purines (9 member)
Adenine
Guanine
pyrimidine (6 member)
Cytosine
Thymine Uracil (found only RNA)

BASE Pairing
Fig 2.10
•A=T
•G=C
DNA is Double
Stranded Helix

. nucleotide
sugar (ribose for RNA or Deoxyribose for DNA )
phosphate base Fig 2.10a

• Backbone -
[deoxyribose sugar-P]n
– anti parallel
orientations
– 5'-3'/ 3'-5'
• Bases inside (planar)
• Ladder steps
• Base pairing
• A=T
• G=C

Self-Tests
• A bond formed by sharing electrons
in the outermost shell.
• Covalent bond
• A bond formed by the gain or loss of
electrons from the outer electron
shell.
• Ionic bond

Figure 5.26 The components of nucleic acids
Figure 5.27 The DNA double helix and its replication
Figure 5.25 DNA ® RNA ® protein: a diagrammatic overview of information flow in a cell

Biological processes are regulated by the action of enzymes. Enzymes as proteins that act as catalysts. The importance of enzymes is lowering activation energy so that the chemical reactions necessary to support life can proceed sufficiently quickly and within an acceptable temperature range. The mode of action of enzymes in terms of the formation of an enzyme - substrate complex.

The way enzymes work can also be shown by considering the energy changes that take place during a chemical reaction. We shall consider a reaction where the product has a lower energy than the substrate, so the substrate turns into the product. Before it can change into the product, the substrate must overcome an “energy barrier” called the activation energy (EA).

Enzymes are biological catalysts in the human body also enzymes are proteins. Proteins are important compounds in living organisms - not just enzymes but in other ways. There are about 40,000 enzymes in a human cell each controlling a different chemical reaction. They increase the rate of reaction but decrease activation energy as it’s a barrier for the enzymes.

Enzymes make it possible for chemical reactions to take place at normal temperatures. The temperature in the human body is about 350c. If the activation energy is high the enzyme reactions will be slower and the body will feel this, this is why the enzymes lower the activation levels otherwise the body temperature will drop.

Enzyme molecules have a complex tertiary structure. The substrate molecules of the enzyme must be precisely the right shape to fit it into part of the molecule called the active site. The substrate molecules are attracted to the active site and form an enzyme - substrate complex. This complex only exists for a fraction of a second, this is when the products of the reaction form. The activation energy is low in this reaction because it is controlled by enzymes and little energy is needed to bring the two substrate molecules together.

The covalent bonds holding the three phosphates together are indicated by a squiggle ~~ and are called high energy bonds. When one is broken, about 7 kcal/mole of energy is released...about twice the activation energy of an average chemical reaction in the cell.
ATP---->ADP +P + energy (~~) ADP + P + energy (~~)-----> ATP

Dehydration /condensation synthesis //hydrolysis animations
http://science.nhmccd.edu/biol/dehydrat/dehydrat.html

ATP
The energy stored in the chemical bonds of fat and starch is converted to ATP. Cells use ATP to drive active transport across membranes, power movement, provide activation energy for chemical reactions and grow.
There are 3 sub-units...a 5 carbon ribose, adenine and a triphosphate group.

Energy
Energy stored in chemical bonds may be transferred to other new chemical bonds by the electrons shifting from one energy level to another.
When an atom loses an electron, it is said to be oxidized, or that oxidation has occurred.
When an atom/molecule gains an electron, it is said to be reduced/reduction.
When these electrons pass from one atom to another, they can carry with them the potential energy of position, maintaining their distance from the nucleus.